For each sample set, we first provide a summary plot of ΔH12 (H12 in susceptible samples subtracted from that in resistant samples) across the genome, with ΔH12 shown in green and the results of the 200 randomisations shown behind in grey. Windows identified as peaks are highlighted by points, colour-coded by whether they are significantly higher than expected based on the simulations (green) or not (purple). For each significant window (green points), we then provide its own plot showing the significant (P < 0.01) SNPs found in the region of that window, and their -log10(Pvalue) of association with phenotype. Red points indicate non-synonymous SNPs, blue points indicate all other SNPs. Point shape indicates whether the mutant allele at that SNP is associated with increased (circle) or decreased (triangle) resistance. Dark points in the centre of the plot show SNPs within the significant window, light points on the sides show SNPs in the region 10,000 bp either side of the window.
Legend
Avrankou_coluzzii_Delta
Baguida_gambiae_Delta
Korle-Bu_coluzzii_Delta
Madina_gambiae_Delta
Obuasi_gambiae_Delta
Baguida_gambiae_PM
Korle-Bu_coluzzii_PM
Madina_gambiae_PM
Obuasi_gambiae_PM
Avrankou_coluzzii_Delta_2L:3627850
Avrankou_coluzzii_Delta_2L:39336219
Avrankou_coluzzii_Delta_2L:40020139
Avrankou_coluzzii_Delta_2R:55812794
Avrankou_coluzzii_Delta_3R:46530542
Avrankou_coluzzii_Delta_3R:46606399
Avrankou_coluzzii_Delta_3R:46697535
Avrankou_coluzzii_Delta_3R:46784988
Avrankou_coluzzii_Delta_3R:46831369
Avrankou_coluzzii_Delta_3R:46856221
Avrankou_coluzzii_Delta_3R:48501462
Baguida_gambiae_Delta_2L:20037401
Baguida_gambiae_Delta_2R:3042129
Baguida_gambiae_Delta_2R:3519707
Korle-Bu_coluzzii_Delta_2R:28546290
Korle-Bu_coluzzii_Delta_2R:54064272
Korle-Bu_coluzzii_Delta_3R:4030785
Korle-Bu_coluzzii_Delta_X:15661082
Madina_gambiae_Delta_2L:14217696
Madina_gambiae_Delta_2L:14284997
Madina_gambiae_Delta_2L:27986348
Madina_gambiae_Delta_2L:28023911
Madina_gambiae_Delta_2L:28093738
Madina_gambiae_Delta_2L:28110739
Madina_gambiae_Delta_2L:28130562
Madina_gambiae_Delta_2L:28174232
Madina_gambiae_Delta_2L:31419497
Madina_gambiae_Delta_2L:3246748
Madina_gambiae_Delta_2L:3287434
Madina_gambiae_Delta_2L:3626021
Madina_gambiae_Delta_X:14215545
Obuasi_gambiae_Delta_2L:25666039
Obuasi_gambiae_Delta_2L:47246666
Obuasi_gambiae_Delta_2R:3175305
Obuasi_gambiae_Delta_2R:40905141
Obuasi_gambiae_Delta_3R:10633692
Obuasi_gambiae_Delta_X:15939854
Baguida_gambiae_PM_2L:19523767
Baguida_gambiae_PM_2L:3266679
Baguida_gambiae_PM_2L:3471571
Baguida_gambiae_PM_2L:3517468
Baguida_gambiae_PM_2L:3578649
Baguida_gambiae_PM_2R:28578188
Baguida_gambiae_PM_2R:28622655
Korle-Bu_coluzzii_PM_2L:22237788
Korle-Bu_coluzzii_PM_2L:23989307
Korle-Bu_coluzzii_PM_2L:28414771
Korle-Bu_coluzzii_PM_2L:28438932
Korle-Bu_coluzzii_PM_2L:28561906
Korle-Bu_coluzzii_PM_2L:28615047
Korle-Bu_coluzzii_PM_2L:28641468
Korle-Bu_coluzzii_PM_2L:28664089
Korle-Bu_coluzzii_PM_2L:28689296
Korle-Bu_coluzzii_PM_2L:36913180
Korle-Bu_coluzzii_PM_2L:36939137
Korle-Bu_coluzzii_PM_2L:36963255
Korle-Bu_coluzzii_PM_2L:37011181
Korle-Bu_coluzzii_PM_2L:37103650
Korle-Bu_coluzzii_PM_2L:37142451
Korle-Bu_coluzzii_PM_2L:37176411
Korle-Bu_coluzzii_PM_2L:37570900
Korle-Bu_coluzzii_PM_2L:3821991
Korle-Bu_coluzzii_PM_3R:4253878
Korle-Bu_coluzzii_PM_X:15614925
Madina_gambiae_PM_2L:31835378
Madina_gambiae_PM_2L:32812183
Madina_gambiae_PM_2L:39511138
Madina_gambiae_PM_2L:41724046
Madina_gambiae_PM_2R:3004025
Madina_gambiae_PM_2R:3037081
Madina_gambiae_PM_3R:28433993
Madina_gambiae_PM_3R:28591533
Obuasi_gambiae_PM_2R:3979039
Obuasi_gambiae_PM_3L:11361643
Obuasi_gambiae_PM_3L:11384773
Obuasi_gambiae_PM_X:13850824
Obuasi_gambiae_PM_X:14004692
